This review describes how metabolomic analysis has been used in support of nutritional research in companion animals, focusing on healthy dogs and cats, and highlights issues that may help those considering metabolomics to support traditional nutritional studies in other mammalian species. Factors that influence the plasma and urinary metabolome in companion animals are known, and include the individual, breed, gender, neuter status, life stage and environment, including diet. Many of these effectors can be controlled or accounted for and it is possible to consider metabolomics as an approach to investigate nutritional status using appropriate study designs. Whilst some research objectives may benefit from taking a discovery approach, the investment in time and resource to generate hypotheses using metabolomics needs to be justified through a good study design with clear objectives and a long-term commitment to the research area to invest in the necessary follow-up studies. As such, whilst metabolomics has immense potential value, the strategic application of it to best serve nutritional sciences requires further development. Different metabolomics study designs and the collection of relevant metadata are discussed to assist those considering nutritional metabolomics.